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Supplementary Materials Journal of Fungi New Method for identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lene Lange1, Kristian Barrett2, and Anne S. Meyer2 1 BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark; [email protected] (L.L) 2 Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; [email protected] (KB), [email protected] (ASM) Table S1. List of the rank of all 1.932 fungal species/strains with regard to biomass degrading capacity based on bioinformatics analysis of their genome sequence. The species are ranked with regard to the Total number of “Function;Family” observations, yet specifying the total number of “Function;Family” observations in each substrate category. The data shown is the full list of data supporting Table 1 in the main manuscript. ACC Submitter Total Xylan Xylan Lignin Pectin Cellulose No Species Class Phylum 1 Pecoramyces ruminatium Neocallimastigo Chytridio 248 85 208 0 541 GCA_000412615.1 Oklahoma State University 2 Neocallimastix californiae Neocallimastigo Chytridio 232 122 172 0 526 GCA_002104975.1 DOE Joint Genome Institute 3 Mycena citricolor Agarico Basidio 91 204 50 149 494 GCA_003987915.1 Universidade de Sao Paulo 4 Verticillium longisporum Sordario Asco 139 176 74 95 484 GCA_001268165.1 SLU 5 Coniochaeta sp. 2T2.1 Sordario Asco 117 102 108 98 425 GCA_009194965.1 DOE Joint Genome Institute 6 Paramyrothecium roridum Sordario Asco 106 163 63 79 411 GCA_003012165.1 USDA, ARS, NCAUR 7 Cadophora sp. DSE1049 Leotio Asco 105 138 75 91 409 GCA_003073865.1 DOE Joint Genome Institute 8 Diaporthe ampelina Sordario Asco 116 129 58 97 400 GCA_001630405.1 Bangalore University 9 Diaporthe longicolla Sordario Asco 111 128 56 90 385 GCA_000800745.1 Purdue University 10 Diaporthe sp. NJD1 Sordario Asco 111 118 58 94 381 GCA_013842865.1 Anhui Agricultural University 11 Diaporthe capsici Sordario Asco 107 118 58 93 376 GCA_013364905.1 Sichuan agricultural university Faculty of Science, Mahidol 12 Diaporthe sp. HANT25 Sordario Asco 106 123 57 88 374 GCA_013435955.1 University Manaaki Whenua Landcare 13 Lachnum nothofagi Leotio Asco 92 124 60 95 371 GCA_003988875.1 Research Central South University of 14 Colletotrichum camelliae Sordario Asco 90 139 65 77 371 GCA_011947485.1 Forestry and Technology 1 15 Colletotrichum truncatum Sordario Asco 90 150 59 72 371 GCA_014235925.1 University of Salamanca University of Agriculture, 16 Colletotrichum sp. COLG25 Sordario Asco 90 139 63 76 368 GCA_009801095.1 Faisalabad Pakistan. 17 Colletotrichum tropicale Sordario Asco 89 139 63 77 368 GCA_013201785.1 RIKEN 18 Colletotrichum fructicola Sordario Asco 89 137 62 77 365 GCA_000319635.2 RIKEN Plant Science Center 19 Colletotrichum asianum Sordario Asco 89 136 61 78 364 GCA_009806415.1 Northwest A&F University Institute of Bioinformatics and 20 Phialocephala subalpina Leotio Asco 96 118 62 87 363 GCA_900073065.1 Systems Biology Institute of microbiology, 21 Pestalotiopsis fici Sordario Asco 92 128 63 80 363 GCA_000516985.1 chinese academy of sciences 22 Colletotrichum siamense Sordario Asco 87 137 62 76 362 GCA_013390195.1 RIKEN 23 Colletotrichum gloeosporioides Sordario Asco 90 134 59 76 359 GCA_003243855.1 Nanjing Forestry University 24 Colletotrichum viniferum Sordario Asco 88 135 59 77 359 GCA_013201765.1 RIKEN 25 Neopestalotiopsis sp. 37M Sordario Asco 96 118 54 89 357 GCA_011058875.1 University of Campinas University of Agriculture, 26 Colletotrichum sp. COLG31 Sordario Asco 92 132 55 78 357 GCA_009800995.1 Faisalabad Pakistan. Central South University of 27 Colletotrichum karsti Sordario Asco 90 139 57 71 357 GCA_011947395.1 Forestry and Technology 28 Colletotrichum aenigma Sordario Asco 86 131 62 75 354 GCA_013390185.1 RIKEN RIKEN Center for Life Science 29 Memnoniella echinata Sordario Asco 99 123 60 67 349 GCA_001599555.1 Technologies, Division of Genomic Technologies 30 Aspergillus latus Eurotio Asco 95 137 53 58 343 GCA_013306195.1 Vanderbilt University Chinese Academy of 31 Clonostachys rosea Sordario Asco 95 121 67 56 339 GCA_000963775.2 Agricultural Sciences Max Planck Genome Center 32 Colletotrichum tofieldiae Sordario Asco 89 116 57 71 333 GCA_001618725.1 Cologne 33 Colletotrichum musicola Sordario Asco 86 125 53 67 331 GCA_014235935.1 University of Salamanca 34 Colletotrichum musae Sordario Asco 82 118 52 77 329 GCA_002814275.1 CAPES 35 Exidia glandulosa Agarico Basidio 82 61 70 114 327 GCA_001632375.1 DOE Joint Genome Institute 36 Nectria sp. B-13 Sordario Asco 94 124 59 50 327 GCA_002682825.1 Anhui University Tianjin Institute of Plant 37 Colletotrichum scovillei Sordario Asco 83 118 57 69 327 GCA_011075155.1 Protection 38 Colletotrichum simmondsii Sordario Asco 81 118 59 66 324 GCA_001563135.1 Universidad de Salamanca 39 Chalara longipes Leotio Asco 94 82 69 79 324 GCA_009732865.1 DOE Joint Genome Institute 40 Colletotrichum plurivorum Sordario Asco 82 125 49 67 323 GCA_014235945.1 University of Salamanca 41 Colletotrichum acutatum Sordario Asco 82 115 57 69 323 GCA_001593745.1 Seoul National University Beltsville Agricultural Research 42 Diaporthe aspalathi Sordario Asco 90 108 47 78 323 GCA_001447215.1 Center RIKEN Center for Life Science 43 Pestalotiopsis sp. JCM 9685 Sordario Asco 89 104 49 81 323 GCA_001599175.1 Technologies, Division of Genomic Technologies Max Planck Genome Center 44 Colletotrichum incanum Sordario Asco 85 115 54 68 322 GCA_001625285.1 Cologne 2 Wageningen University & 45 Verticillium zaregamsianum Sordario Asco 100 124 49 47 320 GCA_002851755.1 Research 46 Colletotrichum nymphaeae Sordario Asco 80 116 57 66 319 GCA_001563115.1 Universidad de Salamanca 47 Colletotrichum coccodes Sordario Asco 85 114 52 67 318 GCA_002249775.1 USDA-ARS 48 Colletotrichum fioriniae Sordario Asco 79 117 55 66 317 GCA_002930455.1 VIB 49 Colletotrichum sojae Sordario Asco 79 121 51 65 316 GCA_014235955.1 University of Salamanca 50 Calonectria naviculata Sordario Asco 86 117 53 58 314 GCA_003031705.1 USDA-ARS 51 Ilyonectria destructans Sordario Asco 92 120 40 62 314 GCA_001913115.1 Northeast Normal University 52 Hyaloscypha variabilis Leotio Asco 91 85 64 73 313 GCA_002865655.1 DOE Joint Genome Institute Jet Propulsion Laboratory, 53 Byssochlamys sp. IMV 00045 Eurotio Asco 88 103 54 66 311 GCA_001931905.2 California Institute of Technology US Department of Agriculture, 54 Fusarium sp. NRRL 22101 Sordario Asco 92 104 46 67 309 GCA_013010345.1 Agriculture Research Service 55 Colletotrichum salicis Sordario Asco 77 114 48 68 307 GCA_001563125.1 Universidad de Salamanca RIKEN Center for Life Science 56 Gliomastix tumulicola Sordario Asco 83 108 63 53 307 GCA_001599755.1 Technologies, Division of Genomic Technologies US Department of Agriculture, 57 Fusarium decemcellulare Sordario Asco 76 119 50 62 307 GCA_013266205.1 Agriculture Research Service AIT-Austrian Institute of 58 Dactylonectria torresensis Sordario Asco 78 128 48 52 306 GCA_011426275.1 Technology 59 Calonectria pseudoturangicola Sordario Asco 85 110 52 58 305 GCA_013403825.1 FABI National Institute of Biological 60 Colletotrichum sp. JS-367 Sordario Asco 80 109 52 64 305 GCA_003122705.1 Resources 61 Penicillium sp. CF01 Eurotio Asco 88 110 37 67 302 GCA_005250745.1 INAIL-Research Area Wageningen University & 62 Verticillium klebahnii Sordario Asco 90 116 49 46 301 GCA_002851715.1 Research 63 Colletotrichum capsici Sordario Asco 74 120 52 55 301 GCA_011947275.1 KLEF Deemed to be University 64 Corynespora cassiicola Dothideo Asco 81 100 44 76 301 GCA_900169545.1 UNIVERSITY OF BRISTOL Nakdonggang National Institute 65 Articulospora tetracladia Leotio Asco 75 122 46 58 301 GCA_003415645.1 of Biological Resources 66 Dactylonectria macrodidyma Sordario Asco 76 123 49 52 300 GCA_000935225.1 USDA-ARS University of California, 67 Hortaea werneckii Dothideo Asco 80 98 62 59 299 GCA_002127715.1 Riverside Wageningen University & 68 Verticillium albo-atrum Sordario Asco 92 114 46 47 299 GCA_002851705.1 Research 69 Colletotrichum trifolii Sordario Asco 74 116 49 60 299 GCA_004367215.1 RIKEN 70 Phaeoacremonium minimum Sordario Asco 84 94 63 57 298 GCA_000392275.1 UC Davis Kunming University of Science 71 Hymenopellis chiangmaiae Agarico Basidio 77 70 44 104 295 GCA_003314085.1 and Technology 72 Fusarium sp. JS1030 Sordario Asco 72 110 53 60 295 GCA_000966855.1 Seoul National University Wageningen University & 73 Verticillium tricorpus Sordario Asco 86 114 50 45 295 GCA_002851695.1 Research 3 The University of Texas Health 74 Pezicula radicicola Leotio Asco 78 103 30 83 294 GCA_003008705.1 Science Center at Houston Chinese Academy of 75 Colletotrichum destructivum Sordario Asco 77 110 46 61 294 GCA_009900065.1 Agricultural Sciences Wageningen University & 76 Verticillium isaacii Sordario Asco 87 112 50 45 294 GCA_002851775.1 Research 77 Colletotrichum sidae Sordario Asco 73 114 47 59 293 GCA_004367935.1 RIKEN 78 Colletotrichum spinosum Sordario Asco 74 113 47 59 293 GCA_004366825.1 RIKEN 79 Zopfia rhizophila Dothideo Asco 85 78 56 74 293 GCA_010093925.1 DOE Joint Genome Institute University of Natural Resources 80 Aspergillus sp. MA 6041 Eurotio Asco 78 104 46 64 292 GCA_003138005.1 and Life Sciences, Vienna Ophiognomonia clavigignenti- 81 Sordario Asco 77 94 46 75 292 GCA_003671545.1 Colorado State U juglandacearum 82 Piromyces sp. E2 Neocallimastigo Chytridio 128 47 117 0 292 GCA_002157105.1 JGI 83 Calonectria leucothoes Sordario Asco 77 105 51 58 291 GCA_002179835.1 USDA-ARS 84 Colletotrichum orbiculare Sordario
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  • The Phylogeny of Plant and Animal Pathogens in the Ascomycota

    The Phylogeny of Plant and Animal Pathogens in the Ascomycota

    Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus.
  • <I>Neolecta Vitellina

    <I>Neolecta Vitellina

    ISSN (print) 0093-4666 © 2011. Mycotaxon, Ltd. ISSN (online) 2154-8889 MYCOTAXON http://dx.doi.org/10.5248/118.197 Volume 118, pp. 197–201 October–December 2011 Neolecta vitellina, first record from Romania, with notes on habitat and phenology Vasilică Claudiu Chinan 1* & David Hewitt 2 1Faculty of Biology, Alexandru Ioan Cuza University, Bd. Carol I, No. 20A, 700505, Iaşi, Romania 2Department of Botany, Academy of Natural Sciences 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103 USA * Correspondence to: [email protected] Abstract — Neolecta vitellina, one of the rarely collected ascomycete species in Europe, is reported from Romania for the first time. The species was found on the ground, under Norway spruce (Picea abies) in 2004, from the Nature Reserve “Tinovul Mare” Poiana Stampei (Eastern Carpathians, Romania). Subsequent field observations have confirmed the presence of Neolecta vitellina in the same location, in the period 2005–10. A description and photographs of the specimens are presented. Key words — Ascomycota, Neolectaceae, ITS sequence Introduction The genus Neolecta Speg. belongs to the ascomycete family Neolectaceae (Redhead 1977), order Neolectales (Landvik et al. 1993), class Neolectomycetes (Taphrinomycotina, Ascomycota). This genus includes three accepted species —N. flavovirescens Speg., N. irregularis (Peck) Korf & J.K. Rogers, N. vitellina— with clavate, unbranched to lobed yellow ascomata, up to about 7 cm tall (Landvik et al. 2003). Of these three species, only N. vitellina has been reported from Europe (Bresadola 1882, Geitler 1958, Hansen & Knudsen 2000: 48–50, Krieglsteiner 1993: 421, Landvik et al. 2003, Ohenoja 1975, Redhead 1989). Work published by European researchers about Neolecta vitellina refers mainly to phylogeny, morphology and ultrastructure (Landvik 1996, 1998; Landvik et al.